Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
REST

Cell type

Cell type Class
Kidney
Cell type
293
Primary Tissue
Kidney
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
HEK293T cells
tissue
kidney
age
fetus
chip antibody
NRSF (Millipore, 17-641 )

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. ChIP-Seq libraries were prepared according to the manual of VAHTSTM Universal DNA Library Prep Kit for Illumina® V2 (ND606). Briefly, DNA was end-repaired using End Prep Mix 3, ligated with index-contained adapters using Rapid DNA ligase in Rapid Ligation buffer, amplificated using PCR Primers and Amplification Mix for libraries. The library fragments of ~350 bp (insert plus adaptor and PCR primer sequences) were isolated with Agencourt® AMPure® XP (Beckman Coulter®). Library DNAs were sequenced on an Illumina HiSeq platform.

Sequencing Platform

instrument_model
HiSeq X Ten

hg38

Number of total reads
28837649
Reads aligned (%)
83.9
Duplicates removed (%)
15.2
Number of peaks
4275 (qval < 1E-05)

hg19

Number of total reads
28837649
Reads aligned (%)
83.2
Duplicates removed (%)
15.4
Number of peaks
3657 (qval < 1E-05)

Base call quality data from DBCLS SRA